After researching which of my special bridges should go where (never really got a good answer, but I have some good guesses) and making sure all the strings were the same tension (thank goodness for a tuning peg koto so I can do it myself.) I got the bridges in the right place for one of the many standard tunings and I'm thrilled! Since you can get the accidentals, you tune it so that all the notes are "valid" so anything you play sounds really awesome and Japanese. I picked out Sakura easily and with no problem. Plus the song book that came with it has sakura, so now I can backwards engineer the music a little bit.
I found some damage and I'm not sure if I did it or if was there to start with. It's just a bridge dent. A very bad picture to show how tall this thing is: